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annotate nanonet_1D.py @ 0:decd5688d719 draft

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planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
author jdv
date Wed, 30 Aug 2017 02:53:02 -0400
parents
children 3f35881c2e25
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
parents:
diff changeset
1 #!/usr/bin/env python3
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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2
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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3 import sys, os
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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4 import glob
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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5 import tarfile
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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6 import subprocess
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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7 import shutil
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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8 import h5py
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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9 import numpy as np
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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11 def main():
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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12 tar_file = sys.argv[1]
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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13 out_file = sys.argv[2]
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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14 threads = sys.argv[3]
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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16 extract_fast5(tar_file)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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18 subprocess.call(["nanonetcall",
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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19 "--jobs", threads,
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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20 "--fastq",
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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21 "--output", out_file,
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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22 "in_dir" ])
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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23
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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24 def extract_fast5(fn):
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
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decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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26 try:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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27 in_dir = "in_dir"
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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28 if not os.path.exists(in_dir):
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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29 os.makedirs(in_dir)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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30
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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31 tar = tarfile.open(fn, mode='r')
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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32 tar.extractall(path=in_dir)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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33
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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34 files = glob.glob(
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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35 os.path.join(in_dir, "**", "*.fast5"),
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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36 recursive=True
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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37 )
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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38 if len(files) < 1:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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39 raise ValueError('No FAST5 files found')
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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40 for f in files:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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41 shutil.copy(f, in_dir)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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42
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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43 except OSError as e:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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44 print("Unexpected error:", e.strerror)
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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45 raise
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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46
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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47 except:
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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48 print("Unexpected error:", sys.exc_info()[0])
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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49 raise
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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50
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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51 if __name__ == "__main__" :
decd5688d719 planemo upload for repository https://github.com/jvolkening/galaxy-tools/tree/master/tools/nanonet commit bf5788ad5a3293446a50a3246b44ba09174c9b71
jdv
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52 main()